Binding Affinity Prediction in Protein-Protein Complexes Using Convolutional Neural Network

Bogdanova, Elizaveta A.; Novoseletsky, Valery N.; Shaitan, Konstantin V.

doi:10.1007/978-3-031-44865-2_42

Studies in Computational Intelligence

2023

DOI: 10.1007/978-3-031-44865-2_42

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Binding Affinity Prediction in Protein-Protein Complexes Using Convolutional Neural Network

Elizaveta A. Bogdanova,

Valery N. Novoseletsky,

Konstantin V. Shaitan

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2024

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Assessment of Binding Affinity in the Complexes of CoV-S-Protein’s RBD and the ACE2 Using Convolutional Neural Networks

Bogdanova,

Chernukhin,

Shaitan

et al. 2024

Biofizika

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The experimentally obtained structures of 48 complexes of the ACE2 receptor with the S protein’s RBD of the coronaviruses SARS-CoV and SARS-CoV-2 (including mutant forms of the latter) were assessed and the dissociation constant was calculated for them. Prediction of binding affinity was carried out using ProBAN, a neural network algorithm, previously developed by the authors, and a number of other algorithms for estimating the Gibbs free energy such as Prodigy, FoldX, DFIRE and RosettaDock. A comparison of the evaluation results shows that ProBAN has the best prediction quality (Pearson correlation − 0.56, MAE − 0.7 kcal/mol) of all the analyzed algorithms. The results obtained suggest better quality of affinity prediction for other protein-protein complexes. Information about the complexes under study and prediction results are available in the repository at the link: https://github.com/EABogdanova/ProBAN_RBD-ACE2.

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Assessment of Binding Affinity in the Complexes of CoV-S-Protein’s RBD and the ACE2 Using Convolutional Neural Networks

Bogdanova,

Chernukhin,

Shaitan

et al. 2024

Biofizika

View full text Add to dashboard Cite

show abstract

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Binding Affinity Prediction in Protein-Protein Complexes Using Convolutional Neural Network

Cited by 1 publication

References 10 publications

Assessment of Binding Affinity in the Complexes of CoV-S-Protein’s RBD and the ACE2 Using Convolutional Neural Networks

Assessment of Binding Affinity in the Complexes of CoV-S-Protein’s RBD and the ACE2 Using Convolutional Neural Networks

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